The invasion of ship domain stands out as a significant factor contributing to the risk of collisions during vessel navigation. However, there is a lack of research on the mechanisms underlying collision risks specifically related to merchant and fishing vessels in coastal waters. This study proposes an assessment method for collision risks between merchant and fishing vessels in coastal waters and validated through a comparative analysis through visualization. First of all, the operational status of fishing vessels is identified. Collaboratively working fishing vessels are treated as a unified entity, expanding their ship domain during operation to assess collision risks. Secondly, to quantify the collision risk between ships, a collision risk index (CRI) is proposed and visualized based on the severity of collision risk. Finally, taking the high risk area of merchant and fishing vessels collision in the Minjiang River Estuary as an example, this paper conduct the analysis involves classifying ship collision scenarios, extracting risk data under different collision scenarios, and visually analyzing areas prone to danger. The results indicate that this method effectively evaluates the severity of collision risk, and the identified high-risk areas resulting from the analysis is verified by accidents occurred in the recent three years.